GenBank as a source to monitor and analyze Host-Microbiome data.
GenBank as a source to monitor and analyze Host-Microbiome data.
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GenBank 作为监测和分析宿主微生物组数据的来源。
DOI：
10.1093/bioinformatics/btac487
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Sarkar,IndraNeil
中科院分区：
文献类型：
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作者：
Ramanan,Vivek;Mechery,Shanti;Sarkar,IndraNeil
微生物组数据集通常受到测序限制的约束。GenBank是最大的公开可用DNA序列的集合，由国家生物技术信息中心（NCBI）维护。基因库记录的元数据在很大程度上是一种未充分研究的资源，可以独特地利用它来获取之前针对微生物组组成的研究总和。在这里，我们开发了一个计算管道来分析GenBank元数据，包含关于宿主，微生物及其起源地的数据。这项工作提供了第一次机会，利用基因库的整体来阐明组成数据的做法，形状如何形成微生物组数据集，以及检查主机微生物组relationships.ResultsThe收集的数据集包含多个王国的微生物，包括细菌，病毒，古菌，原生动物，真菌和无脊椎动物寄生虫，和主机的多个分类类，包括哺乳动物，鸟类和鱼类。该数据集的人类数据子集提供了对当前微生物组数据收集差距的见解，这些数据收集偏向于临床相关病原体。聚类和遗传分析揭示了使用这些数据来模拟宿主分类和进化的潜力，揭示了由宿主饮食，环境和共同进化形成的分组。https://github.com/bcbi/genbank_holobiome GenBank加载程序可在https://github.com/bcbi/genbank_loader.Supplementary上获得。补充数据可在Bioinformaticsonline上获得。
MotivationMicrobiome datasets are often constrained by sequencing limitations. GenBank is the largest collection of publicly available DNA sequences, which is maintained by the National Center of Biotechnology Information (NCBI). The metadata of GenBank records are a largely understudied resource and may be uniquely leveraged to access the sum of prior studies focused on microbiome composition. Here, we developed a computational pipeline to analyze GenBank metadata, containing data on hosts, microorganisms and their place of origin. This work provides the first opportunity to leverage the totality of GenBank to shed light on compositional data practices that shape how microbiome datasets are formed as well as examine host–microbiome relationships.ResultsThe collected dataset contains multiple kingdoms of microorganisms, consisting of bacteria, viruses, archaea, protozoa, fungi, and invertebrate parasites, and hosts of multiple taxonomical classes, including mammals, birds and fish. A human data subset of this dataset provides insights to gaps in current microbiome data collection, which is biased towards clinically relevant pathogens. Clustering and phylogenic analysis reveals the potential to use these data to model host taxonomy and evolution, revealing groupings formed by host diet, environment and coevolution.Availability and implementationGenBank Host-Microbiome Pipeline is available at https://github.com/bcbi/genbank_holobiome. The GenBank loader is available at https://github.com/bcbi/genbank_loader.Supplementary informationSupplementary data are available atBioinformaticsonline.